Hi All,
We were getting this error running cufflinks with a bam file
[ross@bioinfo tophat_test]$ cufflinks accepted_hits.bam
You are using Cufflinks v1.1.0, which is the most recent release.
Warning: BAM header too large
File accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
[14:16:27] Inspecting reads and determining fragment length distribution.
SAM error on line 1678: CIGAR op has zero length
SAM error on line 2017: CIGAR op has zero length
SAM error on line 2025: CIGAR op has zero length
...............
..........
....
I have edited the hits.cpp file (line 590) in the source files from:
static const unsigned MAX_HEADER_LEN = 4 * 1024 * 1024; // 4 MB
to
static const unsigned MAX_HEADER_LEN = 7 * 1024 * 1024; // 7 MB
and ran "make" again. It seems to have fixed the problem.
Would appreciate if anyone has a link to the BAM file format. This edit may cause a problem later on. Had a bit of a hunt around, but can't see it.
Thanks
Ross
We were getting this error running cufflinks with a bam file
[ross@bioinfo tophat_test]$ cufflinks accepted_hits.bam
You are using Cufflinks v1.1.0, which is the most recent release.
Warning: BAM header too large
File accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
[14:16:27] Inspecting reads and determining fragment length distribution.
SAM error on line 1678: CIGAR op has zero length
SAM error on line 2017: CIGAR op has zero length
SAM error on line 2025: CIGAR op has zero length
...............
..........
....
I have edited the hits.cpp file (line 590) in the source files from:
static const unsigned MAX_HEADER_LEN = 4 * 1024 * 1024; // 4 MB
to
static const unsigned MAX_HEADER_LEN = 7 * 1024 * 1024; // 7 MB
and ran "make" again. It seems to have fixed the problem.
Would appreciate if anyone has a link to the BAM file format. This edit may cause a problem later on. Had a bit of a hunt around, but can't see it.
Thanks
Ross
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